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Ma H, Tian Y, Kong D, Guo M, Dai C, Wang Q, Li S, Tian Z, Liu Y, Wei D. One-base-mismatch CRISPR-based transistors for single nucleotide resolution assay. Biosens Bioelectron 2024; 262:116548. [PMID: 38986250 DOI: 10.1016/j.bios.2024.116548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/13/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
An effective strategy for accurately detecting single nucleotide variants (SNVs) is of great significance for genetic research and diagnostics. However, strict amplification conditions, complex experimental instruments, and specialized personnel are required to obtain a satisfactory tradeoff between sensitivity and selectivity for SNV discrimination. In this study, we present a CRISPR-based transistor biosensor for the rapid and highly selective detection of SNVs in viral RNA. By introducing a synthetic mismatch in the crRNA, the CRISPR-Cas13a protein can be engineered to capture the target SNV RNA directly on the surface of the graphene channel. This process induces a fast electrical signal response in the transistor, obviating the need for amplification or reporter molecules. The biosensor exhibits a detection limit for target RNA as low as 5 copies in 100 μL, which is comparable to that of real-time quantitative polymerase chain reaction (PCR). Its operational range spans from 10 to 5 × 105 copy mL-1 in artificial saliva solution. This capability enables the biosensor to discriminate between wild-type and SNV RNA within 15 min. By introducing 10 μL of swab samples during clinical testing, the biosensor provides specific detection of respiratory viruses in 19 oropharyngeal specimens, including influenza A, influenza B, and variants of SARS-CoV-2. This study emphasizes the CRISPR-transistor technique as a highly accurate and sensitive approach for field-deployable nucleic acid screening or diagnostics.
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Affiliation(s)
- Hongwenjie Ma
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China
| | - Yicheng Tian
- Shanghai Medical College, Fudan University, Shanghai, 200031, PR China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China.
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, PR China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China
| | - Qiang Wang
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai Customs PR China, Shanghai, 200335, PR China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, PR China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, PR China.
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2
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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3
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Madahar V, Dang R, Zhang Q, Liu C, Rodgers VGJ, Liao J. Human Post-Translational SUMOylation Modification of SARS-CoV-2 Nucleocapsid Protein Enhances Its Interaction Affinity with Itself and Plays a Critical Role in Its Nuclear Translocation. Viruses 2023; 15:1600. [PMID: 37515286 PMCID: PMC10384427 DOI: 10.3390/v15071600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Viruses, such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect hosts and take advantage of host cellular machinery for genome replication and new virion production. Identifying and elucidating host pathways for viral infection is critical for understanding the development of the viral life cycle and novel therapeutics. The SARS-CoV-2 N protein is critical for viral RNA (vRNA) genome packaging in new virion formation. Using our quantitative Förster energy transfer/Mass spectrometry (qFRET/MS) coupled method and immunofluorescence imaging, we identified three SUMOylation sites of the SARS-CoV-2 N protein. We found that (1) Small Ubiquitin-like modifier (SUMO) modification in Nucleocapsid (N) protein interaction affinity increased, leading to enhanced oligomerization of the N protein; (2) one of the identified SUMOylation sites, K65, is critical for its nuclear translocation. These results suggest that the host human SUMOylation pathway may be critical for N protein functions in viral replication and pathology in vivo. Thus, blocking essential host pathways could provide a novel strategy for future anti-viral therapeutics development, such as for SARS-CoV-2 and other viruses.
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Affiliation(s)
- Vipul Madahar
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Runrui Dang
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Quanqing Zhang
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Department of Botany, College of Natural & Agricultural Sciences, University of California at Riverside, Riverside, CA 92521, USA
| | - Chuchu Liu
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Victor G J Rodgers
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
| | - Jiayu Liao
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
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4
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Liao J, Madahar V, Dang R, Jiang L. Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution. Molecules 2021; 26:molecules26216339. [PMID: 34770748 PMCID: PMC8588070 DOI: 10.3390/molecules26216339] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play pivotal roles in life, and the protein interaction affinity confers specific protein interaction events in physiology or pathology. Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research to detect molecular interactions in vitro and in vivo. The FRET assay provides very high sensitivity and efficiency. Several attempts have been made to develop the FRET assay into a quantitative measurement for protein-protein interaction affinity in the past. However, the progress has been slow due to complicated procedures or because of challenges in differentiating the FRET signal from other direct emission signals from donor and receptor. This review focuses on recent developments of the quantitative FRET analysis and its application in the determination of protein-protein interaction affinity (KD), either through FRET acceptor emission or donor quenching methods. This paper mainly reviews novel theatrical developments and experimental procedures rather than specific experimental results. The FRET-based approach for protein interaction affinity determination provides several advantages, including high sensitivity, high accuracy, low cost, and high-throughput assay. The FRET-based methodology holds excellent potential for those difficult-to-be expressed proteins and for protein interactions in living cells.
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Affiliation(s)
- Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
- Biomedical Science, School of Medicine, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: ; Tel.: +1-951-827-6240; Fax: +1-951-827-6416
| | - Vipul Madahar
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Runrui Dang
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Ling Jiang
- Department of Biochemistry and Molecular Biology, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin 150040, China;
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. SENSORS AND ACTUATORS. B, CHEMICAL 2020; 320:128351. [PMID: 32501366 DOI: 10.1016/j.snb.2020.128391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 05/28/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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6
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Witkowska D. Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction. Molecules 2020; 25:E4133. [PMID: 32927621 PMCID: PMC7571139 DOI: 10.3390/molecules25184133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/01/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Betacoronavirus/chemistry
- Betacoronavirus/pathogenicity
- Binding Sites
- COVID-19
- Coronavirus Infections/epidemiology
- Coronavirus Infections/virology
- Gene Expression
- Host-Pathogen Interactions
- Humans
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/genetics
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/virology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/metabolism
- Severe acute respiratory syndrome-related coronavirus/chemistry
- Severe acute respiratory syndrome-related coronavirus/pathogenicity
- SARS-CoV-2
- Sequence Alignment
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/virology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Danuta Witkowska
- Institute of Health Sciences, Opole University, Katowicka 68, 45-060 Opole, Poland
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7
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Meinke JL, Simon AJ, Wagner DT, Morrow BR, You S, Ellington AD, Keatinge-Clay AT. Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors. ACS Synth Biol 2019; 8:2017-2024. [PMID: 31469555 DOI: 10.1021/acssynbio.9b00047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteins of trans-acyltransferase modular polyketide synthases (PKSs) self-organize into assembly lines, enabling the multienzyme biosynthesis of complex organic molecules. Docking domains comprised of ∼25 residues at the C- and N-termini of these polypeptides (CDDs and NDDs) help drive this association through the formation of four-helix bundles. Molecular connectors like these are desired in synthetic contexts, such as artificial biocatalytic systems and biomaterials, to orthogonally join proteins. Here, the ability of six CDD/NDD pairs to link non-PKS proteins is examined using green fluorescent protein (GFP) variants. As observed through size-exclusion chromatography and Förster resonance energy transfer (FRET), matched but not mismatched pairs of Venus+CDD and NDD+mTurquoise2 fusion proteins associate with low micromolar affinities.
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